X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=c8b2270d685a9d8c1f79904818397452f96827fc;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=b006c895d35dde64bebc18b6229fcd165b71e9d5;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index b006c89..c8b2270 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -33,7 +33,7 @@
- Fetch Sequence
Shows
a dialog window in which you can retrieve known ids from
- Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
+ UniProt, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
Web Services provided by the European Bioinformatics
Institute. See Sequence
Fetcher
@@ -133,10 +133,9 @@
- Load Features / Annotations
Load files describing precalculated sequence features or alignment annotations.
+ href="../features/featuresFormat.html">sequence
+ features or alignment
+ annotations.
- Close (Control W)
Close
the alignment window. Make sure you have saved your
@@ -196,7 +195,7 @@
"Deselect All" to deselect all columns.
- Remove Right (Control R)
If the alignment has marked columns, the alignment will
- be trimmed to the left of the leftmost marked column. To
+ be trimmed to the right of the rightmost marked column. To
mark a column, mouse click the scale bar above the
alignment. Click again to unmark a column, or select
"Deselect All" to deselect all columns.
@@ -204,16 +203,14 @@
All columns which only contain gap characters
("-", ".") will be deleted.
You
may set the default gap character in preferences.
+ href="../features/preferences.html">preferences.
- Remove All Gaps (Control Shift E)
Gap characters ("-", ".") will be
deleted from the selected area of the alignment. If no
selection is made, ALL the gaps in the alignment will be
removed.
You may set the default gap character in preferences.
+ href="../features/preferences.html">preferences.
- Remove Redundancy (Control D)
Selecting this option brings up a window asking you to
@@ -233,8 +230,7 @@
with alignment analysis programs which require 'properly
aligned sequences' to be all the same length.
You
may set the default for Pad Gaps in the preferences.
+ href="../features/preferences.html">preferences.
Select
@@ -278,11 +274,10 @@
WARNING: This cannot be undone.
Select/Hide Columns by Annotation
Select
- or Hide columns in the alignment according to secondary
- structure, labels and values shown in alignment annotation
- rows.
+ href="../features/columnFilterByAnnotation.html">Select/Hide
+ Columns by Annotation
Select or Hide
+ columns in the alignment according to secondary structure,
+ labels and values shown in alignment annotation rows.
View
@@ -310,11 +305,11 @@
- Show Sequence Features
Show
or hide sequence features on this alignment.
- Sequence Feature Settings...
Opens
- the Sequence Feature Settings dialog box to control the
- colour and display of sequence features on the alignment,
- and configure and retrieve features from DAS annotation
+ href="../features/featuresettings.html">Sequence
+ Feature Settings...
Opens the
+ Sequence Feature Settings dialog box to control the colour
+ and display of sequence features on the alignment, and
+ configure and retrieve features from DAS annotation
servers.
- Sequence ID Tooltip
(application only)
This submenu's options allow the
@@ -403,22 +398,21 @@
rendering.
- Wrap
When ticked, the alignment display is "wrapped" to the width of the alignment window. This is
- useful if your alignment has only a few sequences to view
- its full width at once.
+ href="../features/wrap.html">wrapped" to
+ the width of the alignment window. This is useful if your
+ alignment has only a few sequences to view its full width at
+ once.
Additional options for display of sequence numbering
and scales are also visible in wrapped layout mode:
- - Scale Above
- Show the alignment column position scale.
- - Scale Left
- Show the sequence position for the first aligned
- residue in each row in the left column of the alignment.
- - Scale Right
- Show the sequence position for the last aligned
- residue in each row in the right-most column of the
- alignment.
+ - Scale Above
+ Show the alignment column position scale.
+ - Scale Left
Show
+ the sequence position for the first aligned residue in
+ each row in the left column of the alignment.
+ - Scale Right
+ Show the sequence position for the last aligned residue
+ in each row in the right-most column of the alignment.
- Show Sequence Limits
If this box is selected the sequence name will have
the start and end position of the sequence appended to
@@ -474,11 +468,10 @@
colour will be applied to all currently defined groups.
- Colour Text...
Opens the Colour Text
- dialog box to set a different text colour for light and dark
- background, and the intensity threshold for transition between
- them.
+ href="../colourSchemes/textcolour.html">Colour
+ Text...
Opens the Colour Text dialog box
+ to set a different text colour for light and dark background,
+ and the intensity threshold for transition between them.
- Colour Scheme options: None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
@@ -507,8 +500,8 @@
- By Annotation
Colours
the alignment on a per-column value from a specified
annotation. See Annotation Colouring.
+ href="../colourSchemes/annotationColouring.html">Annotation
+ Colouring.
- By RNA Helices
Colours
the helices of an RNA alignment loaded from a Stockholm file.
@@ -563,14 +556,14 @@
provided in this menu.
- Pairwise Alignments
Applies
Smith and Waterman algorithm to selected sequences. See pairwise alignments.
+ href="../calculations/pairwise.html">pairwise
+ alignments.
- Principal Component Analysis
Shows
a spatial clustering of the sequences based on similarity
scores calculated with the alignment. See Principal Component Analysis.
+ href="../calculations/pca.html">Principal
+ Component Analysis.
- Extract Scores ... (optional)
This
option is only visible if Jalview detects one or more
@@ -626,15 +619,14 @@
or elsewhere. You need a continuous network connection in order to
use these services through Jalview.
- - Alignment
- Align the currently selected sequences or all sequences
- in the alignment, or re-align unaligned sequences to the
- aligned sequences. Entries in this menu provide access to the
- various alignment programs supported by JABAWS. See the Multiple
- Sequence Alignment webservice client entry for more
- information.
+ - Alignment
Align the
+ currently selected sequences or all sequences in the
+ alignment, or re-align unaligned sequences to the aligned
+ sequences. Entries in this menu provide access to the various
+ alignment programs supported by JABAWS. See the
+ Multiple Sequence
+ Alignment webservice client entry for more information.
- Secondary Structure Prediction
@@ -667,8 +659,8 @@
- Multi-Harmony
Performs
functional residue analysis on a protein family alignment
with sub-families defined on it. See the Multi-Harmony service entry for more information.
+ href="../webServices/shmr.html">Multi-Harmony
+ service entry for more information.